Biology subjects

Clark, C. J.

Publications and source records attributed to Clark, C. J..

5 recordsLinked to original sources

bioRxiv2026

Pauses in a fast-paced life: Intermittent hovering in hummingbirds

Hummingbirds are known for sustained hovering powered by rapid and continuous wingbeats. Here, we describe and quantify a novel flight behavior, intermittent hovering, in which hovering hummingbirds momentarily pause their wing motion mid-air but maintain their vertical position in space, keeping their wings fully extended at the end of the upstroke. We present the first systematic account of flap-pauses and wing coloration across hummingbirds, and evaluate potential morphological and ecological correlates, as well as evolutionary patterns in the expression of this behavior. Slow-motion footage from 86 species spanning all nine major hummingbird clades shows that at least 45 species exhibited flap-pauses during sustained hovering. Phylogenetic comparative analyses revealed that hovering pauses are evolutionarily conserved and significantly associated with both greater body mass and longer wings. Furthermore, we found that the 16 species in our study with colored underwings also exhibit significantly longer wings. The convergence of intermittent hovering, wing elongation, and chromatic traits leads us to hypothesize that this flight behavior plays a role in visual and/or auditory communication.

evolutionary biology↗

bioRxiv2025

Non-canonical Sodium Channel Isoforms Underlie Chamber Specific Cardiac Excitability

Voltage-gated sodium (NaV) channels drive cardiac excitability. While NaV1.5 is the primary cardiac isoform, the composition and functional contributions of non-NaV1.5 isoforms in the heart remain unclear. Here, we developed a chemical-genetic mouse model (NaV1.5-GX) in which NaV1.5 can be selectively and reversibly inhibited by acyl- and aryl-sulfonamide compounds (GX drugs). NaV1.5-GX mice exhibited normal cardiac function at baseline, but acute GX drug administration caused profound conduction defects and arrhythmias. Whole-heart optical mapping revealed dose-dependent chamber-specific sensitivity to NaV1.5 inhibition, with the right ventricle (RV) being the most sensitive, followed by the left ventricle (LV), left atrium (LA), and right atrium (RA). Patch-clamp recordings of isolated cardiomyocytes with application of NaV isoform-selective inhibitors showed that NaV1.5 contributed 93% of sodium current in the LV, 81% in the RV and 78% in the LA. Non-NaV1.5 isoforms were differentially enriched across chambers: NaV1.8 in the LV, NaV1.1/1.3 in the RV, and NaV1.2/1.6/1.7 in the atria. These results reveal a surprising chamber-specific isoform landscape of cardiac sodium currents which may underlie the right ventricular predominant phenotype of Brugada syndrome and highlight non-NaV1.5 isoforms as potential mediators of chamber-specific cardiac pathologies and as pharmacological targets.

physiology↗

bioRxiv2024

Estimating wingbeat frequency on hummingbirds by using a no-labeling learning computer vision approach

SynopsisWingbeat frequency estimation is an important aspect for the study of avian flight, energetics, and behavioral patterns, among others. Hummingbirds, in particular, are ideal subjects to test a method for this estimation due to their fast wing motions and unique aerodynamics, which results from their ecological diversification, adaptation to high-altitude environments, and sexually selected displays. Traditionally, wingbeat frequency measurements have been done via "manual" image/sound processing. In this study, we present an automated method to detect, track, classify, and monitor hummingbirds in high-speed video footage, accurately estimating their wingbeat frequency using computer vision techniques and signal analysis. Our approach utilizes a zero-shot learning algorithm that eliminates the need for labeling during training. Results demonstrate that our method can produce automated wingbeat frequency estimations with minimal supervision, closely matching those performed by trained human observers. This comparison indicates that our method can, in some scenarios, achieve low or zero error compared to a human, making it a valuable tool for flight analysis. Automating video analysis can assist wingbeat frequency estimation by reducing processing time and, thus, lowering barriers to analyze biological data on fields such as aerodynamics, foraging behavior, and signaling.

bioinformatics↗

bioRxiv2023

Beta-subunit-eliminated eHAP expression (BeHAPe) cells reveal new properties of the cardiac voltage-gated sodium channel

Voltage-gated sodium (NaV) channels drive the upstroke of the action potential and are comprised of a pore-forming -subunit and regulatory {beta}-subunits. The {beta}-subunits modulate the gating, trafficking, and pharmacology of the -subunit. These functions are routinely assessed by ectopic expression in heterologous cells. However, currently available expression systems may not capture the full range of these effects since they contain endogenous {beta}-subunits. To better reveal {beta}-subunit functions, we engineered a human cell line devoid of endogenous NaV {beta}-subunits and their immediate phylogenetic relatives. This new cell line, {beta}-subunit-eliminated eHAP expression cells (BeHAPe), were derived from haploid eHAP cells by engineering inactivating mutations in SCN1B, SCN2B, SCN3B, SCN4B, MPZL1, MPZL2, MPZL3, MPZ and JAML. In diploid BeHAPe cells, the cardiac NaV -subunit, NaV1.5, was highly sensitive to {beta}-subunit modulation and revealed that each {beta}-subunit and even MPZ imparted unique gating properties. Furthermore, combining {beta}1 and {beta}2 with NaV1.5 generated a sodium channel with hybrid properties, distinct from the effects of the individual subunits. Thus, this approach revealed an expanded ability of {beta}-subunits to regulate NaV1.5 activity and can be used to improve the characterization of other /{beta} NaV complexes.

biophysics↗

bioRxiv2022

Tuning aromatic contributions by site-specific encoding of fluorinated phenylalanine residues in bacterial and mammalian cells

The aromatic side-chains of phenylalanine, tyrosine, and tryptophan interact with their environments via both hydrophobic and electrostatic interactions. Determining the extent to which these contribute to protein function and stability is not possible with conventional mutagenesis. Serial fluorination of a given aromatic is a validated method in vitro and in silico to specifically alter electrostatic characteristics, but this approach is restricted to a select few experimental systems. Here, we report a new group of pyrrolysine-based aminoacyl-tRNA synthetase/tRNA pairs that enable the site-specific encoding of a varied spectrum of fluorinated phenylalanine amino acids in E. coli and mammalian (HEK 293T) cells. By allowing the cross-kingdom expression of proteins bearing these unnatural amino acids at biochemical scale, these tools will enable deconstruction of biological mechanisms which utilize aromatic-pi interactions in structural and cellular contexts. Statement of SignificanceThe aromatic side-chains of phenylalanine, tyrosine, and tryptophan are crucial for protein function and pharmacology due to their hydrophobic and electrostatic contributions to catalytic centers and ligand-binding pockets. However, few experimental approaches can chemically assess the functional roles of aromatics in cellular environments. The accepted computational method for aromatic interrogation is via serial fluorination, which lacks an experimental correlate in bacterial or mammalian cell systems. We have identified a family of synthetases to encode multiple different types of fluorinated phenylalanine residues in E. coli and HEK cells via nonsense suppression. The efficiency of these synthetases is sufficient to support biochemical characterization and structural determination of proteins with site-specific incorporation of unnatural phenylalanine analogs.

biochemistry↗